Paleomicrobiology is a part of general microbiology that aims to describe microbial flora (including bacteria, archaea, viruses, parasites, and microscopic fungi) in older specimens; it includes the retrospective diagnosis of infectious and tropical diseases (1, 2). There is no precise numerical definition of an old specimen; we consider as paleomicrobiological specimens any specimen older than 100 years, while the study of more recent samples may be called meso-microbiology. Also, we will consider in this chapter only animal and human specimens, excluding inanimate environmental specimens. The initial works of paleopathology, which used molecular biology techniques based on PCR, highlighted the possibility of the contamination of old samples by contemporary human DNA, casting doubt on the validity of PCR-based work for the detection of human and microbial ancient DNA (aDNA). These doubts, arising in the field of human aDNA, were then relayed to the field of paleomicrobiology by colleagues not practicing microbiology and without microbiological knowledge, who simply derived doubts from their observations of old human DNA. In fact, microbial contamination of an ancient specimen can take place in situ from the surrounding flora, which can be either ancient flora contemporary with the sample or flora from operators at the time of excavation and storage of the old material or during laboratory manipulations, which is modern contamination. Contamination can occur with whole organisms or biomolecules of interest, such as nucleic acids or proteins or mycolic acids (Fig. 1). Indeed, several methods are now used for discovering microbes in ancient specimens beyond the now-conventional aDNA analyses (2).

Sources and prevention of contamination of ancient specimens by microbes and microbial products in the common example of buried specimens. Red bars indicate a pathogen present in the specimen at the time of death; blue and green circles indicate environmental microbes naturally contaminating the specimen during taphonomic processes; blue stars and yellow triangles indicate microbial contamination from discoverers of the specimen and fomites.

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Figure 1

Sources and prevention of contamination of ancient specimens by microbes and microbial products in the common example of buried specimens. Red bars indicate a pathogen present in the specimen at the time of death; blue and green circles indicate environmental microbes naturally contaminating the specimen during taphonomic processes; blue stars and yellow triangles indicate microbial contamination from discoverers of the specimen and fomites.